Bar-Joseph Z - Search Results

1

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data.

Schulz MH, Devanny WE, Gitter A, Zhong S, Ernst J, Bar-Joseph Z. Schulz MH, et al. BMC Syst Biol. 2012 Aug 16;6:104. doi: 10.1186/1752-0509-6-104. BMC Syst Biol. 2012. PMID: 22897824 Free PMC article.

2

scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics.

Chen H, Lee YJ, Ovando JA, Rosas L, Rojas M, Mora AL, Bar-Joseph Z, Lugo-Martinez J. Chen H, et al. bioRxiv [Preprint]. 2023 Dec 19:2023.12.18.572269. doi: 10.1101/2023.12.18.572269. bioRxiv. 2023. Update in: Cell Rep Methods. 2024 Oct 21;4(10):100864. doi: 10.1016/j.crmeth.2024.100864 PMID: 38187629 Free PMC article. Updated. Preprint.

3

Detecting m6A RNA modification from nanopore sequencing using a semi-supervised learning framework.

Teng H, Stoiber M, Bar-Joseph Z, Kingsford C. Teng H, et al. bioRxiv [Preprint]. 2024 Jan 7:2024.01.06.574484. doi: 10.1101/2024.01.06.574484. bioRxiv. 2024. Update in: Genome Res. 2024 Nov 20;34(11):1987-1999. doi: 10.1101/gr.278960.124 PMID: 38260359 Free PMC article. Updated. Preprint.

4

Analyzing time series gene expression data.

Bar-Joseph Z. Bar-Joseph Z. Bioinformatics. 2004 Nov 1;20(16):2493-503. doi: 10.1093/bioinformatics/bth283. Epub 2004 May 6. Bioinformatics. 2004. PMID: 15130923 Review.

5

Deconvolving cell cycle expression data with complementary information.

Bar-Joseph Z, Farkash S, Gifford DK, Simon I, Rosenfeld R. Bar-Joseph Z, et al. Bioinformatics. 2004 Aug 4;20 Suppl 1:i23-30. doi: 10.1093/bioinformatics/bth915. Bioinformatics. 2004. PMID: 15262777

6

Clustering short time series gene expression data.

Ernst J, Nau GJ, Bar-Joseph Z. Ernst J, et al. Bioinformatics. 2005 Jun;21 Suppl 1:i159-68. doi: 10.1093/bioinformatics/bti1022. Bioinformatics. 2005. PMID: 15961453

7

Combined static and dynamic analysis for determining the quality of time-series expression profiles.

Simon I, Siegfried Z, Ernst J, Bar-Joseph Z. Simon I, et al. Nat Biotechnol. 2005 Dec;23(12):1503-8. doi: 10.1038/nbt1164. Nat Biotechnol. 2005. PMID: 16333294

8

STEM: a tool for the analysis of short time series gene expression data.

Ernst J, Bar-Joseph Z. Ernst J, et al. BMC Bioinformatics. 2006 Apr 5;7:191. doi: 10.1186/1471-2105-7-191. BMC Bioinformatics. 2006. PMID: 16597342 Free PMC article.

9

Identifying cycling genes by combining sequence homology and expression data.

Lu Y, Rosenfeld R, Bar-Joseph Z. Lu Y, et al. Bioinformatics. 2006 Jul 15;22(14):e314-22. doi: 10.1093/bioinformatics/btl229. Bioinformatics. 2006. PMID: 16873488

10

Reconstructing dynamic regulatory maps.

Ernst J, Vainas O, Harbison CT, Simon I, Bar-Joseph Z. Ernst J, et al. Mol Syst Biol. 2007;3:74. doi: 10.1038/msb4100115. Epub 2007 Jan 16. Mol Syst Biol. 2007. PMID: 17224918 Free PMC article.

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